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Open Access Highly Accessed Research article

Comparing somatic mutation-callers: beyond Venn diagrams

Su Yeon Kim1 and Terence P Speed12

Author Affiliations

1 Department of Statistics, University of California at Berkeley, 367 Evans Hall, Berkeley, CA 94720 USA

2 Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia

BMC Bioinformatics 2013, 14:189  doi:10.1186/1471-2105-14-189

Published: 10 June 2013

Additional files

Additional file 1:

Supplementary tables and figures.

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Additional file 2:

Details of the individual mutations that were detected by a single caller only or missed by a single caller only, among those detected within the 76 genes from 16 LUSC exome-seq pairs. The details include the validation status, detection status based on the four callers, and the signed GATK quality score, sequencing depth, variant allele fraction, measurement of strand bias in the deep-seq, exome-seq and RNA-seq data.

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